from .family_methods import de_novo, mendel_errors, transmission_disequilibrium_test, trio_matrix
from .impex import (
    export_bgen,
    export_elasticsearch,
    export_gen,
    export_plink,
    export_vcf,
    get_vcf_header_info,
    get_vcf_metadata,
    grep,
    import_avro,
    import_bed,
    import_bgen,
    import_csv,
    import_fam,
    import_gen,
    import_gvcf_interval,
    import_lines,
    import_locus_intervals,
    import_matrix_table,
    import_plink,
    import_table,
    import_vcf,
    index_bgen,
    read_matrix_table,
    read_table,
)
from .misc import filter_intervals, maximal_independent_set, rename_duplicates, segment_intervals
from .qc import (
    VEPConfig,
    VEPConfigGRCh37Version85,
    VEPConfigGRCh38Version95,
    compute_charr,
    concordance,
    nirvana,
    sample_qc,
    summarize_variants,
    variant_qc,
    vep,
    vep_json_typ,
)
from .relatedness import identity_by_descent, king, pc_relate, simulate_random_mating
from .statgen import (
    _blanczos_pca,
    _hwe_normalized_blanczos,
    _linear_regression_rows_nd,
    _linear_skat,
    _logistic_regression_rows_nd,
    _logistic_skat,
    _pca_and_moments,
    _spectral_moments,
    balding_nichols_model,
    filter_alleles,
    filter_alleles_hts,
    genetic_relatedness_matrix,
    hwe_normalized_pca,
    impute_sex,
    lambda_gc,
    ld_matrix,
    ld_prune,
    linear_mixed_model,
    linear_mixed_regression_rows,
    linear_regression_rows,
    logistic_regression_rows,
    pca,
    poisson_regression_rows,
    realized_relationship_matrix,
    row_correlation,
    skat,
    split_multi,
    split_multi_hts,
)

__all__ = [
    'VEPConfig',
    'VEPConfigGRCh37Version85',
    'VEPConfigGRCh38Version95',
    '_blanczos_pca',
    '_hwe_normalized_blanczos',
    '_linear_regression_rows_nd',
    '_linear_skat',
    '_logistic_regression_rows_nd',
    '_logistic_skat',
    '_pca_and_moments',
    '_spectral_moments',
    'balding_nichols_model',
    'compute_charr',
    'concordance',
    'de_novo',
    'export_bgen',
    'export_elasticsearch',
    'export_gen',
    'export_plink',
    'export_vcf',
    'filter_alleles',
    'filter_alleles_hts',
    'filter_intervals',
    'genetic_relatedness_matrix',
    'get_vcf_header_info',
    'get_vcf_metadata',
    'grep',
    'hwe_normalized_pca',
    'identity_by_descent',
    'import_avro',
    'import_bed',
    'import_bgen',
    'import_csv',
    'import_fam',
    'import_gen',
    'import_gvcf_interval',
    'import_lines',
    'import_locus_intervals',
    'import_matrix_table',
    'import_plink',
    'import_table',
    'import_vcf',
    'impute_sex',
    'index_bgen',
    'king',
    'lambda_gc',
    'ld_matrix',
    'ld_prune',
    'linear_mixed_model',
    'linear_mixed_regression_rows',
    'linear_regression_rows',
    'logistic_regression_rows',
    'maximal_independent_set',
    'mendel_errors',
    'nirvana',
    'pc_relate',
    'pca',
    'poisson_regression_rows',
    'read_matrix_table',
    'read_table',
    'realized_relationship_matrix',
    'rename_duplicates',
    'row_correlation',
    'sample_qc',
    'segment_intervals',
    'simulate_random_mating',
    'skat',
    'split_multi',
    'split_multi_hts',
    'summarize_variants',
    'transmission_disequilibrium_test',
    'trio_matrix',
    'variant_qc',
    'vep',
    'vep_json_typ',
]
